Kaepernick hasn't played in the NFL since the 2016 season, the year he began kneeling during the national anthem to raise awareness about police brutality against African-Americans and other racial injustices.
Now, the company finds itself in the midst of a controversy.
"They always want to be on the leading edge of things and create some type of discussion, so I'm not surprised that Nike would be the one to do it," Nike shopper Steve Warhover said.
Yvette Bugingo also shops at Nike and said she wasn't worried about the move.
"The shoes, they don't change. The colors they give you don't change. The prices don't change," Bugingo said. "So I don't see the big deal."
Boston University advertising professor Chris Cakebread said Nike has, until now, been a traditional brand, which makes the move a bold one.
"They wanted to take a bit of a risk and really kind of raise their awareness out there and say, 'We aren't conservative; we really are part of the notion of what's going on in the marketplace,'" Cakebread said.
The move caught swift pushback on social media, with some claiming to burn their Nike gear in protest.
However, at the St. Francis House, the largest homeless day shelter in Massachusetts, they're hoping those thinking about torching their sneakers will think again.
"I would ask people to please consider donating the shoes, rather than burning them," said Maggie Burns from the St. Francis House. "They will go to great use. Our guests are always in need of new or gently used sneakers."
Employees at the Nike location on Boston's Newbury Street said they haven't had anyone return any sneakers or clothing in response to the ad, but they have received calls from upset customers about the topic.